The program is notable for quickly scanning a user's computer to display the most common locations of malware, rather than relying on a database of known spyware.

Except for a small whitelist of known safe entries, HijackThis does not discriminate between legitimate and unwanted items.

HijackThis attempts to create backups of the files and registry entries that it fixes, which can be used to restore the system in the event of a mistake.

Automated tools also exist that analyze saved logs and attempt to provide recommendations to the user, or to clean entries automatically.

Later versions of HijackThis include such additional tools as a task manager, a hosts-file editor, and an alternate-data-stream scanner.